[BioC] irregular spacing exion miRNA microarry 7th generation

Christine Voellenkle [guest] guest at bioconductor.org
Wed Oct 3 16:54:38 CEST 2012

Dear mailing list,
I am doing dual color hybridization using the last version of the miRNA microarrays from exiqon ("7th generation"). 
Applying the limma package, data are background corrected (normexp) and normalized (global loess), subsequently the 4 duplicates of each miRNA species are correlated (DupCor) and lmfit is performed.

I used the following script, which works fine at least until exiqon version 11, since the 4 replicates are regularly distributed:

# identify differentially expressed genes:
design <- modelMatrix(targets, ref="Control")

#show design

DupCor <- duplicateCorrelation(MA, design, ndups=4, spacing=2340)

CorVal <- DupCor$consensus.correlation

fit <- lmFit(MA, design, weights=MA$Weights, ndups=4, spacing=2340, correlation=DupCor$consensus.correlation)

fit <- eBayes(fit)

top = topTable(fit, adjust="BH", number=2340)

write.table(top, file="toptable.txt", row.names=TRUE, col.names=TRUE, sep="\t")

But the last version of the exiqon arrays have a different design, the spacing of the 4 replicates is not regular any more. 2 of the replicates are located within the same block, then, after a distance of 18 blocks, again 2 replicates in the same block.

Block 	Column 	Row 	Name
11 	7 	8 	hsa-miR-1/mmu-miR-1a-3p
11 	7 	18 	hsa-miR-1/mmu-miR-1a-3p
29 	7 	8 	hsa-miR-1/mmu-miR-1a-3p
29 	7 	18 	hsa-miR-1/mmu-miR-1a-3p

I tried to find a way to do it using the unique genenames for identifying the 4 replicates, but for these I only found the function average replicates (avereps), but it is not exactly what I want.

Does anyone know how to perform DupCor using unique gene names??

Thanks a lot in advance,

 -- output of sessionInfo(): 

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> workdir <-"P:/Area_Sanitaria/Area_Servizi/Ricerca/CARDIO_MOLECOLARE/Christine"
> memory.limit(size = 2000)
[1] 2000
> anname <- "Non-Diabetic.paired_trial_ave.rep"
> #Libraries
> library(Biobase)

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

> library(limma)
> library(marray)
> library(statmod)
> library(arrayQuality)
Loading required package: convert
Loading required package: hexbin
Loading required package: grid
Loading required package: lattice
Loading required package: gridBase
Loading required package: RColorBrewer
Warning message:
replacing previous import ‘summary’ when loading ‘hexbin’ 
> library(annotate)
Loading required package: AnnotationDbi

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